ArticleBriefings in bioinformatics2016
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.
Article in Briefings in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- Detection of known gene fusions in cancer cell lines using whole-genome bisulfite sequencing data.Scientific reports · 2026Article
- EpiExpr: Predicting gene expression using epigenetic data and chromatin interactions.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic Alterations in Perioperative Anaphylaxis Among Chinese Patients: A Case-Control Study Protocol.Health science reports · 2025Article
- Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing.Nature communications · 2025Article
- LncRNA Recognition-Associated CpG Island Detection and Methylation Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform.BMC bioinformatics · 2023Article
- Low guanine content and biased nucleotide distribution in vertebrate mtDNA can cause overestimation of non-CpG methylation.NAR genomics and bioinformatics · 2022Article
- Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies.Small methods · 2022Review
- Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.Computational and structural biotechnology journal · 2022Article
- Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.Briefings in bioinformatics · 2021Article
- EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis.BMC genomics · 2020Article
- Review
- Tools and best practices for retrotransposon analysis using high-throughput sequencing data.Mobile DNA · 2019Article
- A multi-dimensional characterization of anxiety in monozygotic twin pairs reveals susceptibility loci in humans.Translational psychiatry · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Cytosine methylation regulates many biological processes such as gene expression, chromatin structure and chromosome stability. The whole genome bisulfite sequencing (WGBS) technique measures the methylation level at each cytosine throughout the genome. There are an increasing number of publicly available pipelines for analyzing WGBS data, reflecting many choices of read mapping algorithms as well as preprocessing and postprocessing methods. We simulated single-end and paired-end reads based on three experimental data sets, and comprehensively evaluated 192 combinations of three preprocessing, five postprocessing and five widely used read mapping algorithms. We also compared paired-end data with single-end data at the same sequencing depth for performance of read mapping and methylation level estimation. Bismark and LAST were the most robust mapping algorithms. We found that Mott trimming and quality filtering individually improved the performance of both read mapping and methylation level estimation, but combining them did not lead to further improvement. Furthermore, we confirmed that paired-end sequencing reduced error rate and enhanced sensitivity for both read mapping and methylation level estimation, especially for short reads and in repetitive regions of the human genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.